predict_n_coincidence_tmh_peptide: Predict the number of n-mers and the number of n-mers that...

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Predict the number of n-mers and the number of n-mers that overlap with at least one amino acid with a TMH for one peptide.

Description

Predict the number of n-mers and the number of n-mers that overlap with at least one amino acid with a TMH for one peptide.

Usage

predict_n_coincidence_tmh_peptide(
  protein_sequence,
  peptide_length,
  verbose = FALSE,
  ic50_prediction_tool
)

Arguments

protein_sequence	a protein sequence
peptide_length	length of the peptide in amino acids
verbose	set to TRUE for more output
ic50_prediction_tool	tool to predict the IC50 from a peptide. Possible values are: mhcnuggetsr mhcnuggetsr, which uses MHCnuggets mhcnuggetsr netmhc2pan, which uses NetMHC2pam EpitopePrediction uses EpitopePrediction

Value

a tibble with

1. n_spots number of spots for the n-mer

2. n_spots_tmh number of spots that have one amino acid overlapping with a TMH

Author(s)

Richèl J.C. Bilderbeek

Examples

library(pureseqtmr)

if (is_pureseqtm_installed()) {

  protein_sequence <- paste0(
    "MYSFVSEETGTLIVNSVLLFLAFVVFLLV",
    "TLAILTALRLCAYCCNIVNVSLVKPSFYVYSRV"
  )

  predict_n_coincidence_tmh_peptide(
    protein_sequence = protein_sequence,
    peptide_length = 9,
    ic50_prediction_tool = "EpitopePrediction"
  )
}

richelbilderbeek/bbbq documentation built on July 27, 2023, 2:15 a.m.